Boost Library and gromacs 2018

[irudayaf]

Hi,

I am trying to compile CHAP but keep running into one issue after another.

this is the one I am getting with gcc 6.3 and gmx 2019.3

chap/src/analysis-setup/residue_information_provider.cpp:25:0:
chap/include/analysis-setup/residue_information_provider.hpp:67:42: error: ‘TopologyInformation’ in namespace ‘gmx’ does not name a type
         void nameFromTopology(const gmx::TopologyInformation &top); 

I checked gromacs source there is a TopologyIformation class in there, I am assuming the version change should have changed something here.

compile well with gromacs 2018.6. So that is a version change issue for sure.

[Inniag]

Thanks for reporting this issue. What you see is indeed an API break in libgomacs between versions 2018 and 2019. I will hopefully be able to fix this soon, but for the time being a workaround would be to use Gromacs 2018.X (or 2016.X). For those versions of Gromacs I have tests that ensure they are compatible with CHAP.

Could you elaborate on what issue you are seeing with the boost library?

[irudayaf]

Hi Gianni,

Yes switching to 2018.6 solved the problem. The boost library issue was associated with clang++ already reported earlier (related to narrowing).

On a side node the current wobj.py throws error in python3, due to map subscription. An easy fix is to cast all maps as list at every instance. self.__materials[self.__crnt_material]["Ka"] = list(map(float, split_line[1:4])) self.__materials[self.__crnt_material]["Kd"] = list(map(float, split_line[1:4])) self.__materials[self.__crnt_material]["Ks"] = list(map(float, split_line[1:4])) self.__vertices.append(list(map(float, split_line[1:4]))) self.__normals.append(list(map(float, split_line[1:4]))) all_indices = list(map(lambda x: x.split("/"), split_line[1:4])) face["vert_idx"] = list(map(int, list(map(lambda x: x[0], all_indices)))) face["norm_idx"] = list(map(int, list(map(lambda x: x[2], all_indices))))

[Inniag]

OK, I'm glad we narrowed it down to Gromacs version then. I'm currently finishing up another project, but will attempt to properly fix this as soon as possible.

For the Boost/Clang issue people can take a look at ticket #2.

The problem with wobj.py is a good catch. I had so far only used Python2 based PyMOL. I created a separate issue for this (#12). Would this be something you'd feel comfortable creating a pull request for?

[irudayaf]

Hi Gianni,

Sure I can create a pull request. Happy to help, and thanks for putting a comprehensive analysis tool.

Best Jerome

[Inniag]

That's great, your help is much appreciated!

I am rather busy this week, so might not get to look at anything in detail before the weekend.